Fanconi Anemia (FA) is a rare genetic disease characterized by chromosome instability mostly resulting from an improper regulation of FANCD2 monoubiquitination. The E2 ubiquitin conjugating enzyme UBE2T along with a multi-protein E3 ubiquitin-ligase complex containing a catalytic subunit FANCL mediates monoubiquitination of FANCD2. However, the upstream events involved in regulating FANCD2 monoubiquitination remain unclear. Here we report that HHR6, human homologs of the yeast ubiquitin-conjugating enzyme Rad6, regulates FANCD2 monoubiquitination in a manner distinct from that of UBE2T. Indeed, although downregulation of HHR6 compromised FANCD2 monoubiquitination and overexpression of HHR6 enhanced FANCD2 monoubiquitination, HHR6 did not directly interact with FANCL. Cells deficient in HHR6, UBE2T or FANCL did, however, all exhibit similar sensitivities to the DNA crosslinking agent mitomycin C (MMC). As an HHR6-induced increase in oncogenic potential could be partially suppressed by co-expression of non-monoubiquitinated FANCD2, a tight regulation of appropriate levels of monoubiquitinated FANCD2 appears to play an important role in tumor suppression. Thus, these results provide further insights into the regulation of FANCD2 monoubiquitination as well as indicate a common link between the FA-BRCA and HHR6 pathways in the maintenance of genome integrity.